To follow up from the RT ticket...
in reply to Strawberry CPAN.pm wrongly overrides INC in Makefile.PL
A command line provided INC value is part of the officially supported API of ExtUtils::MakeMaker, and is known to override any INC passed to MakeMaker from the Perl code.
This is known and intended (if admittedly somewhat confusing) behaviour.
It is the responsibility of any and all MakeMaker Makefile.PL that make use of the INC type params to themselves check for a command line INC param, remove if from @ARGV, and integrate THEIR INC params into the one provided on the command line.